Background Infection is a major cause of morbidity and mortality in pediatric oncology patients, particularly during periods of neutropenia. While bacterial infections are traditionally considered the most common cause of febrile neutropenia, the increasing use of respiratory pathogen panels (RPPs) for viral detection may challenge this view. Methods A retrospective cohort study was conducted on pediatric oncology patients admitted for febrile neutropenia between 2010 and 2022 at a medium-sized academic center. An RPP was performed on nasal swabs from 196 patients at admission and analyzed using molecular-based polymerase chain reaction. Results were available within 12 hours. Pathogens included in the assay were common respiratory viruses and atypical bacteria. Comparison of the duration of neutropenia, duration of fever, and length of stay was made between patients who had a positive respiratory panel and those who did not, as well as each individual pathogen. Additionally, the frequency of viruses before and after the COVID-19 pandemic was analyzed. Results Viral infections were more common than bacterial infections in this cohort. The effect of the RPP on the length of stay was not statistically significant. Parainfluenza viruses were associated with a longer duration of neutropenia, duration of fever, and length of stay. Logistic regression analysis revealed that community coronaviruses, bacterial infections, and a diagnosis of leukemia also impacted these variables. Conclusions Utilization of RPPs may be useful in the workup of febrile neutropenia by providing data for risk evaluation, predicting clinical outcomes, detecting viruses to implement barrier precautions early, and potentially adjusting antimicrobial usage.